sme 1.12.0

Spatial Model Editor python bindings

Spatial Model Editor

A GUI editor to create and edit spatial SBML models of bio-chemical reactions and simulate them using the dune-copasi solver for reaction-diffusion systems.

Getting started

To get started, download and run the GUI for your operating system

Linux	MacOS Arm64	Windows

Windows Arm64: spatial-model-editor-ARM64.exe

Or take a look at our website or the documentation

Pre-release binaries

Pre-release preview binaries are also available which are built from the main branch and can be used for testing new features before the next release:

• Linux pre-release
• MacOS Arm64 pre-release
• Windows pre-release
• Windows Arm64 pre-release

Note: on linux some additional system libraries are required that may not be installed by default. To install them:

• Fedora/RHEL/CentOS: sudo yum install xcb-util-image xcb-util-keysyms xcb-util-renderutil xcb-util-wm

Contributing

Bug reports and feature requests are very welcome, as are fixes or improvements to the documentation (to edit a page in the documentation, click the 'Edit on GitHub' button in the top right).

If you are interested in contributing code, please see the contributing guidelines.

Dependencies

Spatial Model Editor makes use of the following open source libraries:

• dune-copasi - license: GPL2 + runtime exception

• libSBML - license: LGPL

• Qt - license: LGPL

• QCustomPlot - license: GPL

• spdlog - license: MIT

• fmt - license: MIT

• SymEngine - license: MIT

• LLVM Core - license: Apache 2.0 License with LLVM exceptions

• GNU Multiple Precision Arithmetic Library - license: LGPL

• GNU MPFR - license: LGPL

• Computational Geometry Algorithms Library - license: GPL

• Boost - license: boost

• libTIFF - license: MIT

• Expat - license: MIT

• oneTBB - license: Apache-2.0

• Open Source Computer Vision Library - license: Apache-2.0

• nanobind - license: BSD-style

• Catch2 - license: BSL-1.0

• Cereal - license: BSD

• zlib - license: zlib

• bzip2 - license: BSD-style

• pagmo - license: GPL

• zipper - license: MIT

• LibCombine - license: BSD

• VTK - license: BSD

• scotch - license: CeCILL-C

• nlopt - license: LGPL

Licensing Note

The source code in this repository is released under the MIT license, which is a permissive GPL-compatible license.

The open source libraries that it uses are either also released under a permissive GPL-compatible license, or under a GPL license. As described in the gpl-faq, this means that the work as a whole is then licensed under the GPL.

The Linux and Windows binaries also statically link the CUDA redistributable libraries, which are redistributed in accordance with the NVIDIA CUDA Toolkit End User License Agreement (EULA)